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Include study data from prepublished studies
- [ ] need to sort out how to get and present ancestry information
- [ ] need to sort out how this data will be annotated with EFO terms, e.g. to selec…
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Hi,
I am wondering if you have worked with RFMIx v2 and found a way to convert local ancestry calls into SeqArray GDS files...
The GitHub page says:
Convert local ancestry calls into SeqArray G…
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Hi, I'm wondering if one can use gnomad instead of 1k-genomes for the ancestry estimate. somalier files for thousand genomes are restricted to only 5 superpopulations whereas gnomad has a higher diver…
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It looks like there is a branch `abf/transancestry` that provides the multiancestry PRS functionality included in PRScsx (https://github.com/getian107/PRScsx). In some simple testing this branch appea…
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We should change the ARG tutorial to say that _msprime_'s `record_full_arg` is now simply a shorthand for `additional_nodes = msprime.NodeType.COMMON_ANCESTOR | msprime.NodeType.RECOMBINANT`.
Addit…
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For extra "brainfuck" you could try to use `git log --graph`-like routing to indicate on the left side who inherited from whom.
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Hello,
My input file has 21K snps on CHR 21 for a three-way admixed population. I phase my input data and follow steps necessary before running RFmix V2. However, my output in **.msp.tsv** file con…
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Hi @brentp!
I'm working on a project trying to run some ancestry analysis on single-cell RNAseq samples. I used monovar for the variant calling and then peddy for the ancestry calling. All my sampl…
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Apparently the information can be read from SnapGene `.dna` files as xml. This would be important to do, since it will allow people familiar with SnapGenes' UI to do the cloning there, but still share…
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Hi! Trying to use Loter on Ubuntu 22-04 I found this error:
# Command line output
.local/bin/loter_cli -h
Traceback (most recent call last):
File "/home/leonidax/.local/bin/loter_cli", line 5,…